Re: David Dryden - Searching All of Sequence Space (repost of Sean

Seanpit wrote:
On May 12, 7:28 pm, John Harshman <jharshman.diespam...@xxxxxxxxxxx>
wrote:
It is the minimum size for a system where all the parts have to work
together at the same time in a specific arrangement to perform the
function in question. Your electron transport chain works in
sequence, not at the same time. It is a cascading system that doesn't
have to be very specifically arranged in 3D space either where all of
the parts have a specific orientation relative to all of the other
parts. A similar thing is true of the EcoKI system - as already
explained.
Why do you make these particular qualifications of working at the same
time and in a specific arrangement?

Because, that is what produces a requirement for a larger sequence
space and rarer sequences that would qualify within that space - i.e.,
a much lower ratio of sequences that would qualify to produce this
sort of system vs. those that would not with each increase in the
degree or level of these minimum requirements.

In other words, an increase in these requirements are what cause such
systems to move farther and farther beyond the reach of RM/NS.

On what basis do you make these claims?

and
b) novel function.
A qualitatively novel function is a functional system that did not
exist to any useful level in the historical gene pool in question. It
is not simply a quantitative change in function either. For example
increasing the lactase activity of a lactase enzyme isn't going to get
you a nylonse enzyme. That would require a qualitative change in
function. Also, such a change is not based or does not require the
loss of some pre-existing system or interaction.
So what qualitatively novel functions are present in the vertebrate eye
and human brain?
For the eye: Focusing, image processing, image formation, etc - as
I've already discussed with you at length
Yes, and you always avoid directly answering, at length. All these
functions can arise gradually, and separately. They are also to some
degree sequential, which is supposedly a no-no.

They cannot arise gradually enough . . . That's the point. You're
argument that each gradual step is actually realizable in the
variation contained within a given population simply isn't true. That
is why, even by artificial selection based on phenotype alone, you
could not get from one of your proposed steps to the next in your
story for eye evolution.

I would be interested in any support for any of these claims. Why is my argument not true? Why can't functions arise gradually? (I see you ignored the point about them arising separately, presumably because you know that they appear separately in various living species.)

For the Brain: As I've already told you, I don't know. Why not try
to deal with those systems that we know much more about? You have
this tendency to ask about systems for which we know very little when
you get stuck on much simpler systems that you cannot explain.
I mention this because it's one of the few examples you have actually
given of the sort of system you say can't evolve. If you don't know, why
did you originally bring it up as an example?

I know it is more complex than the flagellum. What I don't know,
adequately to defend that is, is if the human brain is more or less
complex than the ape brain in a qualitative sense.

In other words, you never should have brought it up because it isn't an example of the sort of system you're talking about.

In that many aspects of the whole organism must function at the same
time in specific arrangement while EcoKI does not nor is the largest
example of EcoKI at the minimum size requirement to achieve useful
function of any particular type for which EcoKI can be used.
How have you determined the minimum size requirement to achieve useful
function of any particular type for which EcoKI can be used?

You know that it is not greater than the minimum that is actually
known to exist in a functional state. For example, there are lactases
that are known to be several thousand residues in size. Yet, there
are also lactases that are known to be less than 400aa in size. It is
the minimum size requirement that is important to the concept of
functional complexity - not the maximum known size. Modifications
once the system is discovered in sequence space aren't a problem.

I didn't ask about lactase. I asked about EcoKI. At any rate, your methodology is flawed unless you make the assumption that all possible lactases exist in nature, and are known.

A couple of other systems do not qualify, either because they aren't
complex enough or because they aren't really systems (not sure):
4) the electron transport chain
Cascading system, not specified.
It's not a cascading system in the general biological meaning of the
term. And what exactly isn't specified?
It is a cascading system since not all of the parts work together at
the same time, but work in sequence to produce electron transport.
If that's the definition you want to make up, OK.

It make a big statisical difference when it comes to the minimum
sequence space size needed to contain the entire system.

Does it? How do you know that?

And, the arrangement of the parts, while somewhat specified in linear
arrangement do not require a specific three dimensional arrangement.
I'm not sure this is true. As far as I know, it isn't known whether
there is a particular, necessary 3D arrangement. (Of course they're all
embedded in the mitochondrial membrane, so you might imagine the
arrangement would be more or less 2D.)

That's correct - but it isn't specified in 3D, or really even in a
specific 2D arrangement as is a system like the rotary flagellar
motility system or ATP synthase.

I ask how you know that too.

Beyond this, the electron transport chain has not been shown to evolve
in observable time either.
So far, that's irrelevant. We're merely trying to figure out how to
recognize the sorts of things you say can't evolve. Do you now wish to
add the electron transport chain to the list, or not?

The ETC is not on the list because it is a cascading system. My point
here is that you should at least try to counter with systems that have
actually been observed to evolve unless you have some sort of
statistical reason for your argument besides just-so stories or
arguments for common descent without consideration of the odds of your
mechanism actually doing the job.

You don't understand the question being addressed here. It's not "could the electron transport chain evolve?". It's "what are the characteristics of a Pitman 'system'?". Your point is irrelevant.

5) the Eco KI type I DNA restriction and modification enzyme.
Minimum size requirements less than 1000 fsaars per individual
function - none of which require more than 1000 fsaars working
together at the same time.
Sorry, but how does this make sense when whole organisms are counted as
qualifying? Don't multiple individual functions sometimes add up to a
single overall function?
The concept of functional complexity means that the function in
question can only be produced by multiple parts working in specific
arrangement at the same time.
It seems to me that much of the function of an organism consists of
parts working at different times, though often in a coordinated manner.
Have you really thought this through?

The same thing is true of a car. Most of the parts in your car are
not needed in order for it to get you from point A to point B. The
basic directed motilty function of the car is dependent on a very
stripped down version of what you actually drive. The very same thing
is true of an organism like a human being. Much of the body can be
stripped away without a complete loss of the "human function" - so to
speak.

So how does either a car or a human qualify as a Pitman "system"?

I've already gone over this with you extensively. If you can't see
that there are qualitative functional differences between an eyespot
and a human eye, you're beyond help. A human eye isn't simply more of
whatever is in an eyespot. It is a different arrangement of parts
that produces qualitative differences in vision.
But where in the proposed evolutionary sequence does the difference
arise? I agree that French is qualitatively different from Latin, but
where in language history did this difference arise? Your claim of
qualitative difference, as I understand it, requires that there be no
gradual transition possible between functions, and if there is the
difference would not be qualitative. Is that a correct impression?

That's not correct. Qualitative difference can be achieve with very
small modifications. And, this does in fact happen at low levels of
functional complexity. The realization of a lactase enzyme, which was
not in the genome beforehand, can be realized by a single point
mutation to the ebg sequence which did not have the lactase ability
beforehand. That's a qualitative difference which was and can be
produced very gradually. It is just that such small changes are less
and less likely to produce qualitative differences at higher and
higher levels of functional complexity.

So the existence of qualitative differences is irrelevant to whether a system has a novel function. Why, then, do you harp on them? What is it about the eye that makes it a Pitman system? Or to put it another way, how do you know it's a Pitman system?

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